Facility layout problem, especially with the unequal departmental area (UAFLP), is one of the problems studied in combinatorial optimization and has received the attention of many researchers in the past decade.The research used commonly known problems as a standard problem in facility layout problems.There are some problems that have not found the optimal solution and require a long computation time.This research will develop a mathematical model using Mixed Integer Programming method based on Flexible Bay Structure, one of the common representation models used in UAFLP.This method will meet the constraints that arise throughout the process of forming the result.The goal is to reduce non-feasible solutions to reduce the complexity of possible solutions.Some additional constraint functions will be attempted to be added to the model.Testing is done by comparing the effect of each additional constraint function that has different approaches in cutting the complexity of possible solutions.The comparison result of the combination of the constraint function used indicates which constraint function has a major influence in reducing the computation time of the model.Most of the results of this study approached the best-known results.